Over the past year, the 1000 Genomes Phase 1 haplotypes have been extensively used in many genetic studies, most of the time as reference panel to carry out GWAS imputation. In this paper, we showed that using the SHAPEIT2 phasing model, and integrating phased SNP array data, produces more accurate genotype and haplotype estimates. Using the resulting haplotypes as reference panel for GWAS imputation provides better prediction of untyped variants at rare SNPs and Indels across a range of ancestries and SNP arrays. This highlights the potential of using this new set of haplotypes in future GWAS studies. The new haplotype reference set is available from the website ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/shapeit2_phased_haplotypes/ and our new methods are available from the website http://www.stats.ox.ac.uk/~marchini/#software.
